If you make a mistake and want to modify the box, you can do the following:
Create the Virtualbox VM, but don’t add a disk
Move the Vagrant box’s VMDK file:
mv ~/.vagrant.d/boxes/jruby-centos65/0/virtualbox/box-disk1.vmdk ~/VirtualBox\ VMs/centos65/

Now edit the VM and add the box-disk1.vmdk to as a SATA disk under Storage.
Boot the VM, make the changes, then repeat the post cleanup steps above.
Move the disk back into the box:
mv ~/VirtualBox\ VMs/centos65/box-disk1.vmdk ~/.vagrant.d/boxes/jruby-centos65/0/virtualbox/

To delete the VM in VirtualBox I did remove only, then quit VirtualBox to remove any handlers to the files.